David R Arahal

David R Arahal
University of Valencia | UV · Department of Microbiology and Ecology

Dr

About

145
Publications
30,568
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5,347
Citations
Citations since 2016
59 Research Items
3620 Citations
20162017201820192020202120220200400600800
20162017201820192020202120220200400600800
20162017201820192020202120220200400600800
20162017201820192020202120220200400600800
Introduction
I am interested on the application and implementation of genomic comparative analyses to prokaryotic taxonomy and systematics
Additional affiliations
January 2005 - present
University of Valencia
June 2002 - December 2003
September 1998 - August 2000
Technische Universität München

Publications

Publications (145)
Article
Two strains isolated from a sample of activated sludge that was obtained from a seawater-based wastewater treatment plant on the southeastern Mediterranean coast of Spain have been characterized to achieve their taxonomic classification, since preliminary data suggested they could represent novel taxa. Given the uniqueness of this habitat, as this...
Article
Full-text available
Opinion 112 denies the request to place Seliberia Aristovskaya and Parinkina 1963 (Approved Lists 1980) on the list of rejected names because the information provided is insufficient. For the same reason, Opinion 113 denies the request to reject Shewanella irciniae Lee et al . 2006 and Opinion 114 denies the request to reject the name Enterobacter...
Article
Lacticaseibacillus paracasei INIA P272 and Lacticaseibacillus rhamnosus INIA P344, isolated from breast-fed infants, are two promising bacterial strains for their use in functional foods according to their demonstrated probiotic and technological characteristics. To better understand their probiotic characteristics and evaluate their safety, here w...
Article
Full-text available
In Opinion 103, the request to place the name Spirillum volutans Ehrenberg 1832 (Approved Lists 1980) on the list of rejected names is denied because a neotype may be designated. Similarly, because a neotype may be designated, in Opinion 104 the request to place the name Beijerinckia fluminensis Döbereiner and Ruschel 1958 (Approved Lists 1980) on...
Article
A polyphasic taxonomic study was conducted on three strains isolated from drinking water systems that had previously been deposited as Chryseobacterium species at the Spanish Type Culture Collection in order to complete their classification. Strains CECT 9293 T , CECT 9390 T and CECT 9393 T were isolated from sites in Barcelona, Spain, in the frame...
Article
Following the International Committee on Systematics of Prokaryotes electronic discussion and vote on proposals to resolve the status of the Cyanobacteria in the prokaryotic nomenclature, we announce here the results of the ballot. We also present the emended versions of General Consideration 5 and Rules 18a, 24a and 30, based on the outcome of the...
Article
Full-text available
According to the European Directives (UE) 2020/2184 and 2009/54/EC, which establishes the sanitary criteria for water intended for human consumption in Europe, water suitable for human consumption must be free of the bacterial indicators Escherichia coli, Clostridium perfringens and Enterococcus spp. Drinking water is also monitored for heterotroph...
Article
Following the International Committee on Systematics of Prokaryotes electronic discussion and vote on proposals to include the rank of phylum in the rules of the International Code of Nomenclature of Prokaryotes, we here announce the results of the ballot. We also present draft versions of the emended Rules 5b, 8, 15 and 22, based on the outcome of...
Article
The Editorial Board for the International Code of Nomenclature of Prokaryotes (ICNP) has compiled proposed revisions of the ICNP. As outlined previously (Oren et al., Int J Syst Evol Microbiol 2021;71:004598; https://doi.org/10.1099/ijsem.0.004598) and to comply with Articles 13(b)(4) and 4(d) of the statutes of the International Committee on Syste...
Chapter
Ha.lo.mo.na.da.ce'ae. N.L. fem. n. Halomonas, type genus of the family; –aceae, ending to denote a family; N.L. fem. pl. n. Halomonadaceae, the Halomonas family. Proteobacteria / Gammaproteobacteria / Oceanospirillales / Halomonadaceae The family Halomonadaceae is classified within the order Oceanospirillales in the class Gammaproteobacteria. It co...
Article
Full-text available
Strain CECT 9734 T, a Gram-negative, aerobic, chemoorganotrophic bacterium, motile by polar flagella, was isolated from cultured European seabass, Dicenthrarchus labrax, in Spain. It grows from 5 to 42 ºC, 6–9 pH and 1–12% total salinity. Major cellular fatty acids are C15:0 iso, summed feature 9 (C17:1 iso w9c/C16:0 10-methyl) and C17:0 iso. The g...
Chapter
Ha.lo.mo'nas. Gr. masc. n. hals halos salt; L. fem. n. monas a unit, monad; N.L. fem. n. Halomonas salt (‐tolerant) monad. Proteobacteria / Gammaproteobacteria / Oceanospirillales / Halomonadaceae / Halomonas The genus Halomonas is classified within the family Halomonadaceae and the order Oceanospirillales in the class Gammaproteobacteria. The cell...
Chapter
Gri.mon'ti.a. N.L. gen. n. Grimontia of Grimont, after the French microbiologist P. A. D. Grimont. Proteobacteria / Gammaproteobacteria / Vibrionales / Vibrionaceae / Grimontia The genus Grimontia pertains to the family Vibrionaceae and accommodates three species validly published: Grimontia hollisae, Grimontia marina, and Grimontia celer. “Grimont...
Chapter
En.te.ro.vi'bri.o. Gr. neut. n. enteron intestine; L. masc. n. vibrio that which vibrates; N.L. masc. n. Enterovibrio enteric vibrio. Proteobacteria / Gammaproteobacteria / Vibrionales / Vibrionaceae / Enterovibrio The genus Enterovibrio is classified within the family Vibrionaceae and contains five species that have validly published names: Entero...
Article
Full-text available
The draft genome sequence of Bifidobacterium breve INIA P734, a strain shared by mother and child, is reported. It consists of 50 contigs, with 2,391,925 bp, 2,099 genes, and a G+C content of 58.8%. The genome analysis revealed the absence of antibiotic resistance and pathogenicity-related genes.
Article
The Editorial Board of the International Code of Nomenclature of Prokaryotes here explains the proposed procedure towards the production of the next revision of the Prokaryotic Code, to include public discussion of a draft version, to be prepared by the editors, followed by balloting of the members of the International Committee on Systematics of P...
Preprint
Full-text available
Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are p...
Chapter
Co.be′ti.a. N.L. fem. n. Cobetia named after A. B. Cobet, who originally described the type species as “Arthrobacter marinus.” Proteobacteria / Gammaproteobacteria / Oceanospirillales / Halomonadaceae / Cobetia The genus Cobetia is classified within the family Halomonadaceae and the order Oceanospirillales, in the class Gammaproteobacteria. The cel...
Article
Full-text available
Strain SB0023/3 T, isolated from spores of the arbuscular mycorrhizal fungus Glomus iranicum var. tenuihypharum, was analysed to determine whether it represents a new species. It was studied for its applicability in the field of agriculture to reduce the input of nitrogen fertilizers. Comparative analysis of the 16S rRNA gene sequence shows the str...
Article
The International Committee on Systematics of Prokaryotes has formally made final decisions, taking into account the conclusions of the Judicial Commission, on three pending Requests for an Opinion, thereby allowing the corresponding Opinions to be issued. According to Opinion 100, the request for the recognition of strain A1-86 (=DSM 17629=NCIMB 1...
Article
Strain ISS653T, isolated from Atlantic seawater, is a yellow pigmented, non-motile, Gram-reaction-negative rod-shaped bacterium, strictly aerobic and chemoorganotrophic, slightly halophilic (1-15 % NaCl) and mesophilic (4-37 °C), oxidase- and catalase-positive and proteolytic. Its major cellular fatty acids are iso-C15 : 0, iso-C15 : 0 2-OH, and is...
Article
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A comparative taxonomic study of Halorubrum distributum, Halorubrum terrestre, Halorubrum arcis and Halorubrum litoreum was carried out using different approaches, 16S rRNA gene sequence analysis, multilocus sequence analysis (MLSA), phylogenomic analysis based on the comparison of the core genome, orthologous average nucleotide identity (OrthoANI)...
Article
The International Committee on Systematics of Prokaryotes has formally endorsed the conclusions of the Judicial Commission on three pending Requests for an Opinion, thereby allowing the corresponding Opinions to be issued. According to Opinion 97, the request for the conservation of the name Streptomyces scabies is denied, allowing the continued us...
Article
Strain ISS155T, isolated from surface Mediterranean seawater, has cells that are Gram-reaction-negative, motile, strictly aerobic chemoorganotrophic, oxidase-positive, unable to reduce nitrate to nitrite, and able to grow with cellulose as the sole carbon and energy source. It is mesophilic, neutrophilic, slightly halophilic and has a requirement f...
Article
Full-text available
Lactic acid bacteria (LAB) are indigenous microorganisms that have been involved in food fermentations throughout history to preserve food and also to give special characteristics to them. The traditional fermented foods that are still being elaborated in indigenous populations around the world are a potential source of LAB with important biotechno...
Article
Strain CECT 7735T, a marine Gram-reaction negative, aerobic, non-motile bacterium, was isolated from coastal seawater in Valencia, Spain. Strain CECT 7735T is chemoorganotrophic, mesophilic, slightly halophilic, grows at 15-28 °C but not at 4 or 37 °C, requires seawater for growth and grows up to 6 % salinity. The major cellular fatty acid is summe...
Article
Type strains of species are one of the most valuable resources in microbiology. During the last decade, the Genomic Encyclopedia of Bacteria and Archaea (GEBA) projects at the US Department of Energy Joint Genome Institute (JGI) and their collaborators have worked towards sequencing the genome of all the type strains of prokaryotic species. A new p...
Article
Strain CECT 5091T, an aerobic, marine, Gram-reaction- and Gram-stain-negative, chemoheterotrophic bacterium was isolated from oysters harvested off the Spanish Mediterranean coast. Analysis of the 16S rRNA gene sequence placed the strain within the genus Ruegeria, in the family Rhodobacteraceae, with 16S rRNA gene similarities of 98.7, 98.7 and 98....
Article
The genomes of the type strains of Roseivivax atlanticusand Roseivivax marinus(Rhodobacteraceae, Alphaproteobacteria), were analysed to determine their respective Average Nucleotide Identity (ANI) and in silico DNA-DNA hybridization (DDH) values. These species were proposed and effectively published relatively closely in time (February and August 2...
Article
Three strains, H01100409BT, H01100413B, and H27100402HT, were isolated from several internal organs of diseased redbanded seabream (Pagrus auriga) reared in Andalusia (Southern Spain). All strains were studied by phenotypic, including chemotaxonomy, and genomic characteristics. Phylogenetic analysis based on concatenated sequences of six housekeepi...
Article
Full-text available
A taxogenomic study was conducted to describe two new Thalassobius species and to analyze the internal consistency of the genus Thalassobius along with Shimia and Thalassococcus. Strains CECT 5113 T , CECT 5114, CECT 5118 T , and CECT 5120 were isolated from coastal Mediterranean seawater, Spain. Cells were Gram-negative, non-motile coccobacilli, a...
Article
Full-text available
Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for...
Article
Three bacterial strains were isolated from liver and spleen of diseased farmed redbanded seabream (Pagrus auriga) in south-west Spain. Their partial 16S rRNA gene sequences clustered within those of the genus Photobacterium, showing high similarity (98.6-99.3 %) to the type strains of Photobacterium iliopiscarium, P. piscicola, P. kishitanii, P. aq...
Article
Two bacterial strains, EAod9T and SMJ21T, isolated from salt-marsh plants, were determined to be related to species of the genus Vibriofrom from 16S rRNA sequence comparisons. Their closest phylogenetic relatives are members of the Gazogenes clade, Vibrio mangrovi and Vibrio rhizosphaerae , which show the greatest similarity to the SMJ21TrRNA seque...
Article
Thalassobius gelatinovorus is a member of the family Rhodobacteraceae previously classified in the genera Agrobacterium and Ruegeria. Strain Ahrens B6T (= ATCC 25655T, = B6T, = CECT 4357T, = CIP 105976T, = DSM 5887T, = IAM 12617T, = JCM 20688T, = KCTC 22092T, = LMG 129T, = NBRC 15761T, = NCIMB 2206T) was isolated in 1967 from a sea water sampled in...
Article
Full-text available
The genus Photobacterium, one of the eight genera included in the family Vibrionaceae, contains 27 species with valid names and it has received attention because of the bioluminescence and pathogenesis mechanisms that some of its species exhibit. However, the taxonomy and phylogeny of this genus are not completely elucidated; for example, P. logei...
Article
Full-text available
The synonymy between Vibrio hemicentroti Kim et al. 2013 and Vibrio splendidus (Beijerinck 1900) Baumann et al. 1981 was suggested after a recent multilocus sequence analysis (MLSA) of the Splendidus clade which included both type strains (Pérez-Cataluña et al., 2016). In order to clarify their status, we have determined genomic indexes from whole...
Article
Full-text available
A novel Gram-staining-negative, chemoorganotrophic, moderately halophilic, strictly aerobic bacterium, strain MED121T, was isolated from a seawater sample collected at the Blanes Bay Microbial Observatory in the north-western Mediterranean Sea. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that this bacter...
Chapter
Beij.e.rinck'i.a. N.L. fem. n. Beijerinckia named after M.W. Beijerinck, the Dutch microbiologist (1851–1931). Proteobacteria / Alphaproteobacteria / Rhizobiales / Beijerinckiaceae Straight or slightly curved rods, ∼0.5–2.0 × 1.6–4.5 μm, with rounded ends. Cells occur singly or appear as dividing pairs. Sometimes large, misshapen cells 3.0 × 5.0–6....
Article
A multilocus sequence analysis was undertaken in order to redefine the Splendidus clade of the genus Vibrio, a large group of species containing several pathogenic members that affect fish and shellfish, and are difficult to identify through both phenotypic and genotypic approaches. The study included analysis of partial sequences of recA, gyrB, mr...
Article
A multilocus sequence analysis was undertaken in order to redefine the Splendidus clade of the genus Vibrio, a large group of species containing several pathogenic members that affect fish and shellfish, and are difficult to identify through both phenotypic and genotypic approaches. The study included analysis of partial sequences of recA, gyrB, mr...
Article
Strain 96-237T, a Gram-negative, curved to spiral-shaped motile bacterium, isolated from coastal marine water, was found to be related to Grimontia species by 16S rRNA gene sequence comparison, sharing 98.3 % similarity to Grimontia marina and 98.8 % to Grimontia 'indica' type strains. Phenotypic analysis revealed that strain 96-237T is slightly ha...
Article
Full-text available
Nereida ignava strain 2SM4(T) (= CECT 5292(T) = DSM 16309(T) = CIP 108404(T) = CCUG 49433(T)) is a marine bacterium belonging to the Roseobacter group of the family Rhodobacteraceae within the class Alphaproteobacteria. The strain was isolated from sea water surrounding cultivated oysters 2-3 miles off the Mediterranean coast near Valencia (Spain)...
Article
Shimia marina is a member of the family Rhodobacteraceae described in 2006. Strain CL-TA03T (= CECT 7688T) was isolated from a biofilm formed on an acrylic slide submerged in surface water in a coastal fish farm in Tongyeong, Korea. Here we report the draft genome sequence and annotation of S. marina CECT 7688T which is composed by 4,001,860 bp arr...
Article
Full-text available
Thalassobius mediterraneus is the type species of the genus Thalassobius and a member of the Roseobacter clade, an abundant representative of marine bacteria. T. mediterraneus XSM19T (=CECT 5383T) was isolated from the Western Mediterranean coast near Valencia (Spain) in 1989. We present here the draft genome sequence and annotation of this strain...
Article
Full-text available
We report the draft genome sequence and annotation of Leisingera aquaemixtae CECT 8399T (DDBJ/EMBL/GenBank accession number CYSR00000000) which comprises 4,614,060bp, 4313 protein coding genes, 54 tRNA coding genes and 7 rRNA coding genes. General findings of the annotated genome, such as pigment indigoidine operon, phenylacetate oxidation genes or...
Article
Nautella italica is a member of the family Rhodobacteraceae described in 2009. Strain LMG 24365T (= CECT 7645T, = DSM 26436T, = CCUG 55857T) was isolated from a marine electroactive biofilm growing in a stainless steel cathode exposed to natural water in Genoa, Italy. Strain AD 41 (= CECT 7321) was isolated from water surrounding cultivated gilthea...
Conference Paper
Full-text available
La disponibilidad creciente de secuencias genómicas en las bases de datos públicas es de especial relevancia en la caracterización de microorganismos. Los objetivos de este trabajo fueron el análisis genómico y el estudio genómico comparado de 30 cepas de bacterias marinas (disponibles en la CECT) mediante aplicaciones informáticas integradas en se...
Article
Two strains of Gram-negative, facultative anaerobic, slightly halophilic bacteria, isolated from healthy gilthead sea bream (Sparus aurata) cultured in Spanish Mediterranean fish farms were different from their closest relatives, Vibrio scophthalmi and V. ichthyoenteri, by phenotypic, phylogenetic and genomic standards. The strains were negative fo...
Article
(Free Access until 10 June): http://authors.elsevier.com/a/1QvAw2aR~ND7UU A Multilocus Sequence Analysis (MLSA) was performed on members of the Scophthalmi clade in the genus Vibrio, including type and reference strains of the species V. scophthalmi, V. ichthyoenteri, and 39 strains phenotypically identified as Vibrio ichthyoenteri-like, with the a...
Article
Full-text available
The objective of this study is to improve the viability after freeze-drying and during storage of delicate or recalcitrant strains safeguarded at biological resource centers. To achieve this objective, a joint experimental strategy was established among the different involved partner collections of the EMbaRC project ( www.embarc.eu ). Five bacteri...
Article
Full-text available
Vibrio renopiscarius DCR 1-4-2T (CECT 8603T) and DCR 1-4-12 (CECT 8604) were isolated from healthy gilthead sea bream (Sparus aurata) from Mediterranean fish farms (Castellón, Spain). Their draft genome sequences (30 and 44 contigs, respectively) have 4.3 Mbp and a G+C content of 45.2 mol% and contain almost 3,700 protein-encoding genes.
Poster
Full-text available
Launched in 2012, the pan-European Microbial Resource Research Infrastructure (MIRRI) is part of the BioMedicalResearch Infrastructure (RI) ESFRI landscape. Currently, more than 30 public biorepositories and research institutes from 19 European countries (Figure 1) collaborate to establish MIRRI as a European Research Infrastructure Consortium (ERI...
Article
Average nucleotide identity (ANI) was proposed almost 10 years ago as a means to compare genetic relatedness among prokaryotic strains. It was found that values around 95% corresponded to the 70% DNA-DNA hybridization cut-off value that is widely used to delineate archaeal and bacterial species. ANI calculations are one of the many aspects and appr...
Chapter
The family Rhodobacteraceae can be considered a paradigm of modern taxonomy of prokaryotes. Taking into account the number of species and genera that conforms the family, together with the knowledge about their abundance and vast global distribution, it surprises that most of them have been described relatively recent to our days. Two notable excep...
Article
A multilocus sequence analysis based on partial gyrB, mreB, rpoD and pyrH genes was undertaken with 61 putative V. mediterranei/V. shilonii strains from different hosts (mussels, oysters, clams, coral, fish and plankton) or habitat (seawater and sediment) and geographical origins (Mediterranean, Atlantic and Pacific). A consistent grouping was obta...
Article
Full-text available
Strains CUPV261T and CUPV262 were isolated from ropy natural ciders of the Basque Country, Spain, in 2007. Cells are Gram-stain positive, non-spore-forming motile rods facultative anaerobe and catalase negative. They are obligate homofermentative (final product DL-lactate) and produce exopolysaccharides from sucrose.The phylogenetic analysis based...
Article
Full-text available
Strain R46 (CECT 7668; KCTC 23349), a nomenclatural type of Actibacterium mucosum, was isolated from surface seawater collected at Malvarrosa Beach (Valencia, Spain) in July 2008. The draft genome sequence of strain R46 (approximately 3.72 Mbp) contains 22 scaffolds and 3,619 protein-encoding genes, with a G+C content of 60.8 mol%.